Description
Congratulations on your recent publication in BMC Genomics. I would like to use MetaRon, but there appears to be conflicting information between the MetaRon paper and this repository. The paper states that MetaRon requires Python 3, but the installation prerequisites in this repository state Python 2.7 is needed. Further, your most recent commit is named "python3", so I went ahead with a Python 3 installation.
After resolving an indentation issue...
$ source /programs/miniconda3/bin/activate metaron-2.0
$ metaron --help
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 234
gene_name_scaf, strand, gene_st, gene_end, file_name, scaftig_name, gene_name, scaf_name4dict = data_extraction(gene_file, gene_pred_tool)
^
IndentationError: unexpected indent
... the --help option now works.
$ source /programs/miniconda3/bin/activate metaron-2.0
$ metaron --help
usage: metaron [-h] [-n SAMPLE] [-p PROCESS] [-rt READ_TYPE] [-rl READ_LENGTH]
[-pe1 PAIRED_1] [-pe2 PAIRED_2] [-pm PAIRED_MERGED] [-i IGP]
[-j ISC] [-t TOOL] [-o OUTPUT]
optional arguments:
-h, --help show this help message and exit
-n SAMPLE, --sample SAMPLE
Sample name without any dot, underscore or dash
-p PROCESS, --process PROCESS
1. ago: assembly gene prediction and operon prediciton
2. op: operon prediction only. If 'ago', please
provide the following parameters:
-n,-rl,-rt,[-pe1,pe2|-pm],
-rt READ_TYPE, --read_type READ_TYPE
Enter read type. 'merge' if the reads are paired-end
in two file. 'paired' if the reads are paired-end in
one file.
-rl READ_LENGTH, --read_length READ_LENGTH
Enter 'l'if read length is longer than 128 bases and
'r' if read length is shorter than 128 bases
-pe1 PAIRED_1, --paired_1 PAIRED_1
Enter enter paired read file 1
-pe2 PAIRED_2, --paired_2 PAIRED_2
Enter enter paired read file 2
-pm PAIRED_MERGED, --paired_merged PAIRED_MERGED
Enter the paired end read file if both pairedend reads
are in one file
-i IGP, --igp IGP Select the gene prediction .tab file generated via
MetageneMark or Prodigal
-j ISC, --isc ISC Select the file containing all scaftigs
-t TOOL, --tool TOOL Enter 1 for MetaGeneMark, 2 for Prodigal
-o OUTPUT, --output OUTPUT
Enter output destination folder
But running both the example data and my own data through the op process lead to additional errors.
Error 1
$ metaron --sample ERR022075 --process op --igp /home/metaron/data/ERR022075 --isc /home/metaron/data/ERR022075_scaffold.fa --tool 2 --output ./out/
All parameters checked
Sample name: ERR022075
OUTPUT DIRECTORY: ./out/MetaRon_ERR022075
config_file_check start
/programs/miniconda3/envs/metaron-2.0/bin
config_file_check completed
********************************** METAGENOMIC OPERON PREDICTION **********************************
Formatting assembly file
Traceback (most recent call last):
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 1659, in <module>
main()
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 233, in main
gff2tab(sample_name)
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 444, in gff2tab
writer.writerows(zoo)
TypeError: a bytes-like object is required, not 'str'
It seems like this error with writer.writerows() is documented in StackOverflow: TypeError: a bytes-like object is required, not 'str' in python and CSV
Note that my config.txt file reads:
NNPP2.2_path=/home/metaron/NNPP2.2/bin/fa2TDNNpred-PRO.linux
which points to my local installation of NNPP2.2. I've confirmed that the standalone NNPP2.2 program works fine.
In the absence of a config file, I see a second error that also looks to be caused by python3 trying to compile python2 code:
Error 2
Traceback (most recent call last):
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 1659, in <module>
main()
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 180, in main
config_file_check()
File "/programs/miniconda3/envs/metaron-2.0/bin/metaron", line 1615, in config_file_check
NNPP2_path = raw_input('Enter path for NNPP2.2 directory test2')
NameError: name 'raw_input' is not defined
Again, StackOverflow: How do I use raw_input in Python 3
So, should metaron-2.0 be compiled and run in a python2 environment, despite the documentation in the paper and elsewhere that metaron is written in python3?